Nick Clegg's demand – that judges, not ministers will decide when the special courts are invoked – has not been met, says Labour. Photograph: Andrew Matthews/PA

The former justice secretary Ken Clarke has been accused by Labour of giving a "positively misleading" impression that judges will have the key say in deciding whether new secret courts will be convened to hear sensitive intelligence material.

In a sign that the plans are heading for a rocky parliamentary ride this autumn, the shadow justice secretary, Sadiq Khan, has written to Nick Clegg to say Labour cannot support the plans unless ministers change their "misguided" approach. Khan is intervening days before the Lib Dems debate a motion at their conference in Brighton calling for a watering down of the plans to set up a new generation of secret courts.

The Lib Dem deputy prime minister supports the plans after securing a series of concessions from Clarke, who remains responsible for the bill after he lost his job as justice secretary. These include assurances that the courts will only be used in exceptional cases where there are concerns over national security.

But Khan says that one of Clegg's main demands – that judges, not ministers will decide when the special courts are invoked – has not been met. In his letter, Khan writes: "This is not the judge-led process that Ken Clarke has claimed. In fact, I would go so far as to say that it is positively misleading to claim it is judge-led. Ministers retain the power on what is kept secret – meaning the usual checks and balances that provide proper scrutiny of government action will not be present."

The shadow justice secretary singled out Clarke for criticism after he used a Guardian article this week to claim that judges would have the upper hand in deciding whether sensitive intelligence is placed before the secret courts. "Judges and not the executive will have to take the key decisions about whether a closed hearing is justified," Clarke wrote.

The proposals are designed to ensure that intelligence material that cannot currently be heard in court can be admitted as evidence by restricting its circulation. The intelligence would be heard by a judge but not by claimants or their lawyers.

The bill was drawn up after the public airing of evidence during litigation brought on behalf of Binyam Mohamed and other former Guantánamo Bay detainees. The court of appeal agreed to disclose CIA information which showed that MI5 and MI6 knew Mohamed, a British resident, had been abused.

Khan, who is understood to have been briefed by Clarke on privy council terms, calls on Clegg to give serious consideration to alternatives to the "close material procedures". He writes: "It is simply wrong to claim, as justice ministers do, that if CMPs are not introduced, intelligence officers would be forced to give evidence in public courts. Such claims totally ignore how our current system has different ways of coping with these kinds of circumstances. Rather than a misguided rush to legislation, the government would have been better advised to hold a proper debate about all the options available."